Magnesium in PDB 1q6r: Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Xylulose 5-Phosphate

The structure of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Xylulose 5-Phosphate, PDB code: 1q6r was solved by E.L.Wise, W.S.Yew, J.A.Gerlt, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.29 / 1.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.912, 41.580, 91.627, 90.00, 96.41, 90.00
R / Rfree (%)	19 / 22.9

The binding sites of Magnesium atom in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Xylulose 5-Phosphate (pdb code 1q6r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Xylulose 5-Phosphate, PDB code: 1q6r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Xylulose 5-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Xylulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg7300 b:21.1 occ:1.00 OE2 A:GLU33 1.9 19.7 1.0 OD2 A:ASP62 2.0 24.2 1.0 O A:HOH7442 2.1 20.6 1.0 O2 A:LX17301 2.1 25.6 1.0 O A:HOH7410 2.2 20.8 1.0 O3 A:LX17301 2.2 22.3 1.0 C2 A:LX17301 2.9 26.7 1.0 CD A:GLU33 3.0 21.9 1.0 C3 A:LX17301 3.0 22.1 1.0 CG A:ASP62 3.1 25.9 1.0 OE1 A:GLU33 3.4 23.4 1.0 O4 A:LX17301 3.7 24.5 1.0 CB A:ASP62 3.8 21.4 1.0 NZ A:LYS64 3.9 32.1 1.0 O A:HOH7369 4.0 25.5 1.0 C4 A:LX17301 4.0 22.8 1.0 OD1 A:ASP62 4.1 25.9 1.0 OD1 A:ASP11 4.1 28.4 1.0 C1 A:LX17301 4.2 23.6 1.0 OD2 A:ASP11 4.3 26.0 1.0 CG A:GLU33 4.3 19.4 1.0 CA A:GLY35 4.4 20.2 1.0 O A:HOH7439 4.4 42.0 1.0 OG1 A:THR36 4.5 24.1 1.0 N A:THR36 4.5 21.5 1.0 CG A:ASP11 4.7 26.9 1.0 CB A:ALA9 4.7 20.9 1.0 C5 A:LX17301 4.8 22.3 1.0

Magnesium binding site 2 out of 2 in the Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Xylulose 5-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with Bound L- Xylulose 5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg9300 b:20.0 occ:1.00 OD2 B:ASP62 2.0 22.1 1.0 O B:HOH9453 2.0 23.7 1.0 O2 B:LX19301 2.1 23.1 1.0 OE2 B:GLU33 2.1 19.8 1.0 O B:HOH9384 2.1 19.7 1.0 O3 B:LX19301 2.2 20.7 1.0 C2 B:LX19301 2.8 27.0 1.0 C3 B:LX19301 3.0 23.0 1.0 CD B:GLU33 3.0 18.0 1.0 CG B:ASP62 3.2 24.5 1.0 OE1 B:GLU33 3.4 19.4 1.0 O4 B:LX19301 3.8 23.7 1.0 CB B:ASP62 3.8 22.4 1.0 NZ B:LYS64 3.9 32.1 1.0 C4 B:LX19301 3.9 22.6 1.0 O B:HOH9387 4.1 28.3 1.0 OD1 B:ASP11 4.1 24.4 1.0 OD1 B:ASP62 4.2 23.9 1.0 C1 B:LX19301 4.2 25.2 1.0 OD2 B:ASP11 4.2 23.6 1.0 O B:HOH9386 4.3 38.3 1.0 CG B:GLU33 4.3 15.7 1.0 CA B:GLY35 4.5 17.8 1.0 OG1 B:THR36 4.5 25.2 1.0 CB B:ALA9 4.6 18.4 1.0 N B:THR36 4.6 19.8 1.0 CG B:ASP11 4.7 21.4 1.0 C5 B:LX19301 4.8 21.7 1.0 CE1 B:HIS136 4.9 38.2 1.0

E.L.Wise, W.S.Yew, J.A.Gerlt, I.Rayment. Structural Evidence For A 1,2-Enediolate Intermediate in the Reaction Catalyzed By 3-Keto-L-Gulonate 6-Phosphate Decarboxylase, A Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily Biochemistry V. 42 12133 2003.
ISSN: ISSN 0006-2960
PubMed: 14567674
DOI: 10.1021/BI0348819